ResearchPage - Chijioke

Chijioke's Research

Week 13 -

Protein Enzyme Assay

Absorbance taken @ 410 nm
Molecular Weight: 33512.8 kDa

1st Run (#39-46):
Initial Conc.- .4 mg/mL

A: .000
B: .570
C: 1.103
D: 1.003
E: .950
F: .581
G: .616
H: 1.405

2nd Run (#31-38):
Initial Conc.- .5 mg/mL

A: .000
B: .417
C: .238
D: .325
E: .252
F: .893
G: .617
H: .982

Week 12 -

YopH Virtual Screening

HF9 Library

- #1 best ligand (RH00719SC)


- #2 best ligand (BTB05187SC)


- #3 best ligand (DFP00065SC)


- #4 best ligand (HTS09290SC)


- #5 best ligand (BTB08339SC)


- #6 best ligand (JFD03976SC)


- #7 best ligand (RJF00101SC)


- #8 best ligand (BR00114SC)


- #9 best ligand (HTS11989SC)



- #10 best ligand (CD03598SC)

CB306 Library

- Top 5 Ligands found in library





- #1 best ligand (7575772)



- #2 best ligand (5467784)



- #3 best ligand (7842136)



- #4 best ligand (7726180)



- #5 best ligand (6629394)

Week 11 -

Protein Characterization

Well #1: Marker
Well #2: Sample #0 (A)
Well #3: Sample #1 (A)
Well #4: Sample #2 (Flow Through)
Well #5: Sample #3 (Wash)
Well #6: Sample #4 (Elution #1)
Well #7: Sample #5 (Elution #2)

FPLC

- After running the process, it was found that fractions #31-38 and #39-46 were the best ones for in assay and inhibition.
I later would concentrate each set of fractions for use.

Week 10 -

Protein Purification

- Sample #3 (Flow Through)
- Sample #4 (Wash)
- Sample #5 (Elution #1)
- Sample #6 (Elution #2)

Week 9 -

Protein Expression

- Sample #0 (A & B)
- Sample #1 (A & B)
- Sample #2 [made from combination of A & B samples of #0 and #1]

Week 8 -

pNIC-Bsa4 Cloning

- YopH Master Plate


- pNIC-Bsa4 PCR Cloning Gel


- pNIC-Bsa4 Nanodrop Graph




- Sample 1


- Sample 2 (Take 1)


- Sample 2 (Take 2)


- Sample 3


- Sample 4 (Take 1)


- Sample 4 (Take 2)


- Sample 5 (Take 1)


- Sample 5 (Take 2)


- Sample 6 (Take 1)


- Sample 6 (Take 2)


- Sample 7 (Take 1)


- Sample 7 (Take 2)


- Sample 8 (Take 1)


- Sample 8 (Take 2)

Week 7 -

My samples for cloning were lost this week, so I needed to re-run the procedure again. No results were taken from this week.

Week 6 -

Chijioke - good job. Don't need to show so much of primer design. Maybe just show your final primers (oligos). --Dr. B

PCR Primer Design for Yersinia pestis (YopH)

The oligonucleotide assembly is:
----------------------------------------------------------------
1 10 20 30 40 50 60
| | | | | | |

1 --->
1 ATGCGCGAACGCCCACACACCTCTGGTCACCACGGTGCCGGCGAAGCTCGCGCAACCGC
CGAGCGCGTTGGCGC

M R E R P H T S G H H G A G E A R A T A

| | | | | | |

3 --->
61 aggctcgtgccgaactgtcttctcgtctgacc
GGAAGATGGCAAAGGGGTATGCCAGGCCTCCGAGCACGGCTTGAC
<--- 2
P S T V S P Y G P E A R A E L S S R L T

| | | | | | |

5 --->
121 accctgcgtaataccctggcaccagcaa GCATGTGGT
atgggaccgtggtcgttggttgctgggcgcaatggacgttcgtacacca

T L R N T L A P A T N D P R Y L Q A C G

| | | | | | |


181 GGTGAAAAACTCAACCGCTTCCGTGACATCCAATGCCGTCGTCAGACCGCA
ccactttttga GGCAGCAGTCTGGCGTCAAGCACGC
<--- 4
G E K L N R F R D I Q C R R Q T A V R A

| | | | | | |

7 --->
241 actacatccaggttggtaacactcgcaccatcgcctgccagtacccg
CTAGACTTGCGCTTGATGTAGGTCCAACCATTGTG gggc
<--- 6
D L N A N Y I Q V G N T R T I A C Q Y P

| | | | | | |

9 --->
301 ctgcagtctcaac TGAAAACCGTACCCCGGTTCTG
gacgtcagagttgaccttagagtgaaggcgtacgaccgacttttggcatggggcca
<--- 8
L Q S Q L E S H F R M L A E N R T P V L

| | | | | | |

1
361 GCTGTGCTGGCGTCTTCTTCTGAGATCGCGAATCAGCG c
GACTCTAGCGCTTAGTCGCAAAGCCATACGGCCTGATGAAG

A V L A S S S E I A N Q R F G M P D Y F

| | | | | | |

1 --->
421 cgtcaatctggtacctacggttctatcaccgttgaatccaaaatgacccagcaggtcgg
GCAGTTAGACCATGGATGC tactgggtcgtccagcca
<--- 10
R Q S G T Y G S I T V E S K M T Q Q V G

| | | | | | |

13 --->
481 GACATGTACACCCTGACCATCCGTGAAGCGGGTCAGAAA
gacccactgccatagtaccgcctgtacatgtgggactggtag
<--- 12
L G D G I M A D M Y T L T I R E A G Q K

| | | | | | |

15 --->
541 ACCATCTCTGTTCCGGTTGTT aaaccgccgtttctagc
GGTAGAGACAAGGCCAACAAGTGCAGCCATTGACCGGCCTAGTTTGGCGGCAAAGATCG
<--- 1
T I S V P V V H V G N W P D Q T A V S S

| | | | | | |


601 gaggtcactaaagcgctcgcttctctggttgatcagactgcgg
C gaccaactagtctgacgcctctggtttgcattgtac
4
E V T K A L A S L V D Q T A E T K R N M

| | | | | | |

17 --->
661 TGAATCTAAAGGTTCCTCTGCCGTTGCGGACGACTCCAAACTGCGTCCAGTTATCCAC
atacttagatttccaaggagacgg GACGCAGGTCAATAGGTG
<--- 16
Y E S K G S S A V A D D S K L R P V I H

| | | | | | |

19 --->
721 TG gcagctgatcggtgcgatgtgcatgaacgactct
ACAGCGCGTCCACAACCAGCATGCCGCGTCGACTAGCCACGC
<--- 18
C R A G V G R T A Q L I G A M C M N D S

| | | | | | |

21 --->
781 cgtaactctcagctctctgtcgagga CCAGCGCAATGGT
gagtcgagagacagctcctgtaccaaagagtttacgcacaggtcgcgttacca

R N S Q L S V E D M V S Q M R V Q R N G

| | | | | | |


841 ATTATGGTTCAGAAAGACGAACAGCTGGACGTTCTCATTAAACTGGC
taatacc CCTGCAAGAGTAATTTGACCGCCTTCCGGTCCCG
<--- 20
I M V Q K D E Q L D V L I K L A E G Q G

| | | | | | |


901
GCAGGCGACGACTTGAGAATT
<--- 22
R P L L N S X
----------------------------------------------------------------

Frequency Range Number of Codons
-------------------------------------
0% - 4% 0
5% - 9% 4
10% - 14% 7
15% - 19% 18
20% - 24% 12
25% - 29% 13
30% - 34% 44
35% - 39% 19
40% - 44% 3
45% - 49% 3
>= 50% 184
-------------------------------------
Total Codons Used = 307

Tm Range # of Overlaps
-------------------------------------
<59 0
59 0
60 0
61 10
62 11
63 0
64 0
65 0
66 0
>=67 0
-------------------------------------
Tm Range = 1.9

Ovrlap Len Range # of Oligos
-------------------------------------
<15 1
15 0
16 2
17 4
18 2
19 3
20 5
21 2
22 2
23 0
24 0
>=25 0
-------------------------------------
Lowest Overlap = 14

Length Range # of Oligos
-------------------------------------
<51 0
51-52 0
53-54 0
55-56 1
57-58 0
59-60 21
61-62 0
63-64 0
65-66 0
67-68 0
69-70 0
>=71 0
-------------------------------------
Longest = 60


22 oligonucleotides need to be synthesized
----------------------------------------------------------------
1 ATGCGCGAACGCCCACACACCTCTGGTCACCACGGTGCCGGCGAAGCTCGCGCAACCGC 59
2 CAGTTCGGCACGAGCCTCCGGACCGTATGGGGAAACGGTAGAAGGCGCGGTTGCGCGAGC 60
3 AGGCTCGTGCCGAACTGTCTTCTCGTCTGACCACCCTGCGTAATACCCTGGCACCAGCAA 60
4 AGTTTTTCACCACCACATGCTTGCAGGTAACGCGGGTCGTTGGTTGCTGGTGCCAGGGTA 60
5 GCATGTGGTGGTGAAAAACTCAACCGCTTCCGTGACATCCAATGCCGTCGTCAGACCGCA 60
6 GTGTTACCAACCTGGATGTAGTTCGCGTTCAGATCCGCACGAACTGCGGTCTGACGACGG 60
7 ACTACATCCAGGTTGGTAACACTCGCACCATCGCCTGCCAGTACCCGCTGCAGTCTCAAC 60
8 ACCGGGGTACGGTTTTCAGCCAGCATGCGGAAGTGAGATTCCAGTTGAGACTGCAGCGGG 60
9 TGAAAACCGTACCCCGGTTCTGGCTGTGCTGGCGTCTTCTTCTGAGATCGCGAATCAGCG 60
10 CGTAGGTACCAGATTGACGGAAGTAGTCCGGCATACCGAAACGCTGATTCGCGATCTCAG 60
11 CCGTCAATCTGGTACCTACGGTTCTATCACCGTTGAATCCAAAATGACCCAGCAGGTCGG 60
12 GATGGTCAGGGTGTACATGTCCGCCATGATACCGTCACCCAGACCGACCTGCTGGGTCAT 60
13 GACATGTACACCCTGACCATCCGTGAAGCGGGTCAGAAAACCATCTCTGTTCCGGTTGTT 60
14 CGCTAGAAACGGCGGTTTGATCCGGCCAGTTACCGACGTGAACAACCGGAACAGAGATGG 60
15 AAACCGCCGTTTCTAGCGAGGTCACTAAAGCGCTCGCTTCTCTGGTTGATCAGACTGCGG 60
16 GGCAGAGGAACCTTTAGATTCATACATGTTACGTTTGGTCTCCGCAGTCTGATCAACCAG 60
17 TGAATCTAAAGGTTCCTCTGCCGTTGCGGACGACTCCAAACTGCGTCCAGTTATCCACTG 60
18 CGCACCGATCAGCTGCGCCGTACGACCAACACCTGCGCGACAGTGGATAACTGGACGCAG 60
19 GCAGCTGATCGGTGCGATGTGCATGAACGACTCTCGTAACTCTCAGCTCTCTGTCGAGGA 60
20 CCATAATACCATTGCGCTGGACACGCATTTGAGAAACCATGTCCTCGACAGAGAGCTGAG 60
21 CCAGCGCAATGGTATTATGGTTCAGAAAGACGAACAGCTGGACGTTCTCATTAAACTGGC 60
22 TTAAGAGTTCAGCAGCGGACGGCCCTGGCCTTCCGCCAGTTTAATGAGAACGTCC 55

FINAL SUMMARY FOR 1 SOLUTION
--------------------------------------------------------------------------------
# Tm Len | Score TmRange Short Long #Olig #Repeat #Misprime

1 62 60 | 0.000 1.9 14 60 22 0 0

--------------------------------------------------------------------------------

PCR Overlap

Lane 1: skipped
Lane 2: 100 bp Ladder
Lane 3: Primary (1°) PCR Primer - YopH
Lane 4: Secondary (2°) PCR Primer - YopH


- Nanodrop Graph of PCR² Primer with Yersinia pestis (YopH)

Week 5

Virtual Screening Refresher

- Table of Top 11 Ligands

Top 10 Ligands Images

- BindingDB_50228029, #1 best ligand


- 5193911, #2 best ligand


- 5157370, #3 best ligand


- 5185261, #4 best ligand


- 5224221, #5 best ligand


- 5143470, #6 best ligand


- 5109057, #7 best ligand


- 5186972, #8 best ligand


- 5230391, #9 best ligand


- 5159193, #10 best ligand

Top 3 Ligands

ID: BindingDB_50228029
Mol. Weight: 610.719343
Molecular Formula: C30H31FN4O5S2
Mol. Name: 3-fluoro-N-[1-[5-(4-phenylbutyl)-1H-imidazol-2-yl]-2-[4-(1,1,3-trioxo-1,
2-thiazolidin-5-yl)phenyl]ethyl]benzenesulfonamide
hDon: 3
hAcc: 7

Week 4

PCR pNIC-Bsa4 Gel Run

Lane 1: Skipped
Lane 2: 100 bp Ladder
Lane 3: PCR pNIC-Bsa4 (Highest Conc. of pLIC)
Lane 4: PCR pNIC-Bsa4 (Medium Conc. of pLIC)
Lane 5: PCR pNIC-Bsa4 (Lowest Conc. of pLIC)
Lane 6: PCR pNIC-Bsa4 (No pLIC; Control)

PyMol Refresher

- View of the chains, active sites,and polar contacts in 2H2Q


- View of the chains, active sites,and polar contacts in 3CL9


- View of the chains, active sites,and polar contacts in 1U72


- Combination of the active sites for 1U72 & 3CL9, showing each of their polar contacts


- Four different chains involved in the protein 3HBB


- Comparison of both NAP (MTX) for the 1st chain in 3HBB

Week 3

Submitting DNA Sequence

Forward Reaction

NNNNNNNNNNNNNNNNNNNNNNNNANTGGGCNNGNCGTCNCATGCTCCCGGCCGCCNTGGCCGCGGNNTTTTAGTGANGNTNNNGGNGNNGACCNNNAATGATTCTNATTGNTTGANGGATAANTNNNNNGNNTGNGATCGTTAANCNNNNGNCCNANANGGNTTNTNNGGGAGGCACNNNNAATGCACACTACTTTNANGGCCAAGGCNATGGAAAACGAANNCCTTANGAGGGGGANNANAGGGCAAAGCTNACTGNCACCNANGGTGGACCTCTGCCNTTTGCTTGGGATATTTNATCACCACTGNCTCNANACNGAANCATACNATTNACCNGNNNNCCNGAATACATCCCTGANNATGTAAANCANTCATTCCCTGAGGGATANACATGGGAGAGGATCATGAACTTNNNANATNGNNNGGNGTGTACTGTCNNCNATGATNNCAGNATCNGANGAAACTGNTTNNTCTACNNNNNNCANTNTCNNAAAGTGAANTTTCCNCCCCNTGNACNTGNTATGCNGAAAAANANATNNGCCTGNNAACAANANNNNNANANNCTCNNTNCGNTGGATGNCANGNTCAGCTGAAACNACTTNNNGNNTCTNAAGTTGNNNNNANGTGGTTACAATNTNNGTGAATNNNCTTCTACTGNTGAGCATGNANGNCNGNGNGGACGCNNGGNANANNNNNTNNCCCTCACACTGNNNGTANCCANGCNCGNCNAGGATTNAANATTCGTNGANNNATNNNTAAATATCCNNTGNACGCCGCTCNTNCNNNNTCANCTNCATNNNCATCTNTAAAANNTCNNNANGNNTGNNNNGTCNGGNANCATGNNNNNCNGGNCCAANTCNNGCTCNNNNNGANNNNNANNNNNNNNTTCCTTGGGCCACCGGTTTTCNANNNNNNNNNTNNNNNAAAACTTCGANTTTCCNNNNNATTGNCNANNNNNNTCGTCCCCCNTTCCCNNCNTNGNNNNNNAAN


- Blast made through Nucleotides

Reverse Reaction

NNNNNNNNNNNGGTGANCTATAGAATACTCAAGCTATGCATCCNACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGNGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGANGCCCGCACCGATCGCCNTTCCCANCAGTTGCGCAGCCTGNATGGNGAATGGNCNCNNCCNGNANNGNNCATNAGCGCGNNNNNNNNNNNNCNNNCAGNNNNACGCTANNNTTNCNNCNCNANCNNCGNNCTTNNGNTTNNNNNNTTTNNNNCNNNNTNNCNNTTTCCNTCAGNNNNNNNNGGGNNNNNNTNNNNCNANTNNNNTNNNNNNNNNCNNNNNNNNNNNNGGNNNNNNGNNNNNCNNNNNNNNNNNNNNN


- Human Blast


- Nucleotide Blast

Week 2

Restriction Enzyme Digest

Lane 1: Skipped
Lane 2: 1 kb Ladder
Lane 3: Uncut pGBR-22
Lane 4: EcoRI, cut with pGBR-22 (Tube A)
Lane 5: PvuII, cut with pGBR-22 (Tube B)
Lane 6: EcoRI + PvuII, cut with pGBR-22 (Tube C)

PCR pGBR22 Gel Run

1st Attempt:

Lane 1: Skipped
Lane 2: 100 bp Ladder
Lane 3: PCR pGBR-22 (Tube A), none shown
Lane 4: PCR pGBR-22 (Tube B), none shown
Lane 5: PCR pGBR-22 (Tube C), none shown
Lane 6: PCR pGBR-22 (Tube D), none shown

2nd Attempt:

Lane 1: Skipped
Lane 2: 100 bp Ladder
Lane 3: PCR pGBR-22 (Tube A), none shown
Lane 4: PCR pGBR-22 (Tube B), none shown
Lane 5: PCR pGBR-22 (Tube C), none shown
Lane 6: PCR pGBR-22 (Tube D), none shown

3rd Attempt:



Lane 1: Skipped
Lane 2: 100 bp Ladder
Lane 3: PCR pGBR-22 (Tube A)
Lane 4: PCR pGBR-22 (Tube B)
Lane 5: PCR pGBR-22 (Tube C)
Lane 6: PCR pGBR-22 (Tube D)

Week 1

Analyzing DNA Sequence

VDS4_M13R.. Original Sequence:
`NNNNNNNNNNNTATNGNATACTCAAGCTATGCATCCAACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAANAGGCCCGCACCGATCGCCCTTCCCACAGTTGCGCAGCCTGATGGCNATGGACGCNNCCTGNANCGNCGCATTAGCNCGGCNGGNNNGNGNNCNCGCAGCGNGACNCTACANTTNCNGCNNCNANCNNNNNCNTTCNNTTNTNCNNNTNNNNNNNNNNNNNNNTTNCCGNNAGNTNNAANNGGGGNNNNNNNNNATNNGNTNNNNNNNNNNCCAAANTGNNNGNNNNGNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNGANCNNNNNNNNNNNNANNNNNNNNNNNCNNNNNAANNNNNCCNNTNNN

VDS_M13R.. Without the N’s:
TATNGNATACTCAAGCTATGCATCCAACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAANAGGCCCGCACCGATCGCCCTTCCCACAGTTGCGCAGCCTGATGGCNATGGACGCNNCCTGNANCGNCGCATTAGCNCGGCNGGNNNGNGNNCNCGCAGCGNGACNCTACANTTNCNGCNNCNANCNNNNNCNTTCNNTTNTNCNNNT


Blast #1:



Blast #2:



Comparison to Known DNA:




Translation with the PurpleProteinCodingSequenceforBB.txt:

>rf 1 UntitledMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH* ORF: >1c1|Sequence 1 ORF:105...788 Frame +3ATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAA
Compare Protein Tranlsations:


Lost In Translation:

Translation 1:

>rf 1 UntitledXXXXXXYSSYASNALGALPYGRPAGGRTSDFD*LKEKYHECDR*TNDLQGLYVRHGQWTLL*GRRRWKRKALRGGADGKAHCHQGWTSAICLGYFITTVSIRKHTIHQVP*RHP*LCKAVIP*GIYMGEDHEL*RWCSVYCQQ*FQHPRQLFHLQCQNLWCELSSQWTCYAEEDTGLGTQH*ASLCTRWNADRKQLYGSEVGRRWLLFV*IQIYLQGKEACEDARVSLC*PQTGCNQSQQGLHIC*AV*NIHCTPLFARSSPSPSLKSRGHGGREHATSGPIRPIVSRITIHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVIAXRPAPIALPTVAQPDGXGRXLXRRISXAGXXXRSXTLXXXXXXXXFXXXXXXXXXXPXXXXGXXXXXXXXXPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPX

Translation 2:

>rf 2 UntitledXXXXXXTQAMHPTRWELSHMVDLQAAALVILID*RRNIMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH*NPAAMAAGSMRRRAQFALVVLQFTGRRFTTS*LGKPWRYPT*SPCSTSPFRQLARXGPHRSPFPQLRSLMAMDAXXXXALARXXXXXAAXXYXXXXXXXXSXXXXXXXXXXRXXXXGXXXXXXXXXQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Translation 3:

>rf 3 UntitledXXXYXILKLCIQRVGSSPIWSTCRRPHF*LIEGEIS*V*SLNK*PTRFICQARSMDTTLRSKAMEKESLTRGSRR*SSLSPRVDLCHLLGIFYHHCLNTEAYHSPSTLKTSLIM*SSHSLRDIHGRGS*TLKMVQCVLSAMIPASKATVSSTMSKSLV*TFLPMDLLCRRRHRAGNPTLSVSLHEMECETTLWL*SWKEVVTICVNSNLLTRQRSL*GCQGITMLTANWM*PVTTRITHLLSSVKYPLHATLCSVITITITKIPRPWRPGACDVGPNSPYSESYYNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEXARTDRPSHSCAA*WXWTXPXXXH*XGXXXXXQRDXTXXAXXXXXXXXXXXXXXXXXXXXXGXXXXXXXXXKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Translation with the PurpleProteinCodingSequenceforBB.txt:

>rf 1 UntitledMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH* ORF: >1c1|Sequence 1 ORF:105...788 Frame +3ATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAA

Slicing & Dicing

- DNA cut with only EcoRI


- DNA cut with only PvuII


- DNA cut with both EcoRI & PvuII

Virtual Gel